gnu: Add ocaml-sqlite3.

* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.

gnu: snakemake: Update to 3.11.2.

* gnu/packages/python.scm (snakemake): Update to 3.11.2.

gnu: r-minimal: Fix remaining reproducibility problems.

Fixes <https://bugs.gnu.org/25598>.

* gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining
reproducibility fixes to "build-reproducibly" phase.

gnu: r: Rename to r-minimal.

* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".

gnu: Add r-with-recommended-packages.

* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.

gnu: r: Do not build recommended packages.

* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.

gnu: r-survival: Move to set of recommended R packages.

* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
packages.

gnu: Add r-spatial.

* gnu/packages/statistics.scm (r-spatial): New variable.

gnu: r-rpart: Move to the set of recommended packages.

* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
packages.

gnu: r-nnet: Move to set of recommended R packages.

* gnu/packages/machine-learning.scm (r-nnet): Move from here...
* gnu/packages/statistics.scm (r-nnet): ...to here because the other
recommended R packages are here.

gnu: r-mgcv: Move to set of recommended R packages.

* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
packages.

gnu: Add r-nlme.

* gnu/packages/statistics.scm (r-nlme): New variable.

gnu: r-matrix: Move to set of recommended R packages.

* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
packages.

gnu: r-lattice: Move to other recommended R packages.

* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.

gnu: Add r-kernsmooth.

* gnu/packages/statistics.scm (r-kernsmooth): New variable.

gnu: Add r-foreign.

* gnu/packages/statistics.scm (r-foreign): New variable.

gnu: Add r-codetools.

* gnu/packages/statistics.scm (r-codetools): New variable.

gnu: Add r-cluster.

* gnu/packages/statistics.scm (r-cluster): New variable.

gnu: Add r-class.

* gnu/packages/statistics.scm (r-class): New variable.

gnu: Add r-mass.

* gnu/packages/statistics.scm (r-mass): New variable.